In 1608 Clock became involved in a dispute with the Waterlanders under Denys van Hulle. After he had vainly demanded of van Hulle that he resign his ministry (1611), he parted from him two years later because of difference of opinion on mixed marriages. Hans Matthijs, Jan Schellingwou, Anne Annesz, and Jan Eriksz went with Clock. A new High German congregation was formed in Amsterdam, which was but short-lived. This quarrel was the more lamentable because in 1604 Clock had attempted a reconciliation with all the Flemish, an attempt blocked chiefly by the opposition of Claes Ganglofs and the Groningen congregation. He had better success in his attempt at reconciliation with the Waterlanders in De Rijp under Cornelis Michielsz, who in 1611 had separated from the Bevredigde Broederschap at the instigation of Claes Wolter Kops; but this division was healed in September of the same year at a large conference in Amsterdam. After the division of 1613, both parties preached in the church at Haarlem for a time. After Clock had vainly tried to lock the doors against the opposing party, his party tried to gain possession of the building by illegal methods. The title deed to the church property was made out in the name of Thomas van Dalen. His son Jacob Thomas van Dalen and his son-in-law Guillaume Stoppelaar sold the building on 25 April 1615 to Leenaert Clock; but the opposition prevented the sealing of the transaction. This unedifying quarrel ended in 1617 with the erection of a new building by each party. In the meantime Clock had left Haarlem and was living in Schoonhoven, Dutch province of South Holland, where he became a copreacher of Jan Lammersz. A futile attempt at reconciliation was made in 1621. Clock resisted it, though his daughter Anneken was on the opposing side. The followers of Leenaert Clock in Haarlem, Amsterdam, and elsewhere were called the Afgedeelden. They united with the Flemish in 1639.

Clock's place in Mennonite history rests in the main on his writings, which had lasting influence. As a hymn writer he was very successful, even though Wolkan is right in saying that many of his hymns lack poetic inspiration. This was due chiefly to his favorite practice of composing acrostics, that is, hymns in which the initial letters of each stanza when read together give the name of a person. In the 1625 collection of 435 hymns, no fewer than 398 are of this kind. (Concerning the names see Th. J. J. Arnold in Bibliographische Adversaria II.) But other hymns are of lasting value; and his most popular hymn (No. 131 in the Ausbund) was regularly sung by the Amish as the second hymn in every church service (see J. W. Yoder, Amische Lieder, 1942, No. 1). Clock published the following five hymnbooks: (a) Veelderhande schriftuerlijcke nieuwe Liedekens (Utrecht, 1593, combined with the following); (b) Het groote Liedeboeck (Leeuwarden, 1625); (c) Kleyn Liedtboeck (Haarlem, 1625); (d) Vyftien schriftuerlijcke Liedekens (Amsterdam, 1690); (e) Vier en twintig schriftuerlijcke Liedekens (Amsterdam, 1589). All these books became rather popular and passed through several editions. Some hymns were also translated into German (possibly by the author himself) and were adopted in two leading devotional manuals: the Confession oder kurzes und einfältiges Glaubens-bekenntnis . . . der Gemeinden in Preussen (1751 edition; here we find the hymn, "Lebt friedsam, spricht Christus der Herr"), and Christliches Glaubensbekenntnis, . . . T.T.V.S. (Amsterdam, 1664; see van Sittert), a most popular handbook, which contains seven of Clock's hymns.

But Clock's influence goes still further. In 1625, he published a Forma eenigher Christelijcker Ghebeden (A Formulary of Several Christian Prayers), which until recently was hardly noticed though it proved to be the very standard book upon which all later Mennonite prayer literature is built (Friedmann, Menn. Piety, 181 f.). A German translation of this book appeared in T. T. van Sittert's manual of 1664 with 18 prayers (while the 1751 Prussian manual contains only 13 prayers). The preface says, "To the unanimous brotherhood in Prussia and to the believers everywhere assembled in Christ, dedicated by L. C.," indicating that Clock either had drawn up this prayer formulary expressly for the brethren in Prussia or that he later translated it from the Dutch for their sake. In any case, a few of these prayers became exceedingly popular, particularly the "general" prayers II and III (in van Sittert's manual). It has been proved that prayer II was time and again used and reshaped until it found its final form in the Swiss-Mennonite prayer book, Ernsthafte Christenpflicht of 1739 (Friedmann, 181-192). This is the more surprising as this prayer in its original form is rather colorless. Yet nothing else was available of Mennonite origin, particularly in the German language, for those who wanted a Mennonite prayer book. Thus van Sittert's edition found wide circulation both in the north and in the south of Germany.

In the early controversy of the Dutch Mennonite Church concerning the practice of silent or audible prayers (see Prayer), Clock stood on the side of those who preferred the audible prayer in worship. Knipscheer reports in his fine study of this controversy (Doopsgezinde Bijdragen 1897, 109f.), that Leenaert Clock, who had come from Germany, spoke his prayers always "overloyt," that is, audibly, as Hans de Ries used to do.

Clock had also visited the congregations in Prussia and Poland in 1606. In the quarrel between Clock and Kops in Haarlem the Prussian churches remained neutral.

With regard to Clock's doctrinal stand, Alenson claims that Clock placed great stress on Menno's peculiar doctrine of the incarnation.